Figure 4—figure supplement 1.

(A) Schematic of the reporter construct for enhancer testing. Tol2, transposase integration site. E1b, minimal promoter. GFP, green fluorescent protein. pA, polyadenylation sequence. CFP, cerulean fluorescent protein. (B) Snapshots of genomic regions (gene loci and GRCz10 coordinates listed) for enhancer testing. Peaks (p) tested are shown, with Foxc1-dependent regions in purple and Foxc1-independent elements in green. μATACseq reads are shown in each row for the experiments indicated, with chondrocyte and non-chondrocyte peaks from 72 hpf embryos. DNCCs, dorsal CNCCs. (C) GFP expression (yellow) driven by the indicated peaks in stable transgenic zebrafish at 6 dpf. Confocal projections of the cartilages of the first two arches are shown in lateral view for acan_p1, slc35d1a_p1 and sparc_p1 and ventral view for col9a1a_p1. For acan_p1, sox10:Dsred labels all chondrocytes for reference in magenta. Arrows indicate expression in cartilages. sparc_p1 also drives expression in ligamentocytes and osteoblasts, and slc35d1a_p1 in pharyngeal muscles. (D) Confocal sections of representative embryos injected with enhancer constructs are shown in lateral view at 6 dpf. Mosaic expression in chondrocytes (yellow, arrows) is shown, with DIC (white channel) providing embryo context. Numbers indicate proportion of embryos positive for the co-selectable lens:CFP marker (also on the injected plasmid) in which the displayed patterns were observed. Scale bar = 100 μm.